GMX_distance

User discussions
1

GROMACS version: 2019.3
GROMACS modification: Yes/No
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Hi,
I want to find the distance between the centre of masses of a group of atoms (that I’ve already indexed). The output file gives two values at each time interval. Why two values and what are they meant for?

@ title “Average distance”
@ xaxis label “Time (ns)”
@ yaxis label “Distance (nm)”
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend “com of group “Protein_&r_0&C*HH*&!C” plus com of group “Protein_&r_43&C*HH*&!C””
0.001 3.125
0.001 3.130
0.002 3.168
0.002 2.989
0.003 3.053
0.003 3.076
0.004 3.065

For calculating this I’ve used the command

gmx distance -f protein.xtc -s grompp.tpr -n comindex.ndx -tu ns -oav rl.xvg -select ‘com of group “Protein_&r_0&C*HH*&!C” plus com of group “Protein_&r_43&C*HH*&!C”’.

Thanks in advance
TP

2

Hi,
A couple of question to better understand
Which frequency do you use to save your trajectory? What happens if you remove the option -tu ns ?
Thank you
Best regards
Alessandra

3

Hi Alessandra,
Many thanks for your reply. I saved the trajectory every 0.5ps. As you suggested, on removing the -tu ns flag. It works! The time column is every 0.5 ps. Why is this so?

gmx distance -f protein.xtc -s run_1/grompp.tpr -n comindex.ndx -oav rl_trial.xvg -select ‘com of group “Protein_&r_0&C*HH*&!C” plus com of group “Protein_&r_43&C*HH*&!C”’

gmx distance is part of G R O M A C S:

GROningen Mixture of Alchemy and Childrens’ Stories

@ title “Average distance”
@ xaxis label “Time (ps)”
@ yaxis label “Distance (nm)”
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend “com of group “Protein_&r_0&C*HH*&!C” plus com of group “Protein_&r_43&C*HH*&!C””
0.500 3.125
1.000 3.130
1.500 3.168
2.000 2.989
2.500 3.053
3.000 3.076
3.500 3.065

4

Hi,
the time is reported using only 3 ciphers after dot. Thus when use the option -tu, values that differs of 0.5 ps can not be differentiate.

That is

3.125 is the distance at t= 0.0005 → approx to 0.001
3.130 is the distance at t=0.001

I hope it helps to understand

best regards
Alessandra